Underground solution to starving rice plants

Scientists have pinpointed a gene that enables rice plants to produce around 20% more grain by increasing uptake of phosphorus, an important, but limited, plant nutrient.

The discovery unlocks the potential to improve the food security of rice farmers with the lowest value phosphorus-deficient land, allowing them to grow more rice to add to global production, and earn more.

The gene—called PSTOL1, which stands for phosphorus starvation tolerance—helps rice grow a larger, better root system and thereby access more phosphorus. Farmers can apply phosphorus fertilisers to increase productivity but, on problem soils, phosphorus is often locked in the soil and unavailable to plants.

Also, phosphorus fertiliser is often unaffordable to poor farmers. Adding to the problem is that phosphorus is a non-renewable natural resource and rock phosphate reserves – the source of most phosphorus fertilisers – are running out.

“For many years, we have searched for genes that improve phosphorus uptake,” said Dr. Sigrid Heuer, senior scientist at the International Rice Research Institute (IRRI) and leader of the team that published the discovery in Nature.

“We’ve known for a long time that the traditional rice variety Kasalath from India has a set of genes that helps rice grow well in soils low in phosphorus,” she added.

Kasalath’s superior performance under phosphorus deficiency was initially discovered by Dr. Matthias Wissuwa from the Japan International Research Center for Agricultural Sciences. He then started collaborating with IRRI and shared the DNA information of Kasalath. The current research was supported and facilitated by the CGIAR Generation Challenge Program.

“We have now hit the jackpot and found PSTOL1, the major gene responsible for improved phosphorus uptake and understand how it works,” Heuer said.

According to Dr. Wricha Tyagi at the School of Crop Improvement at the Central Agricultural University in the Indian state of Meghalaya, knowledge of the exact gene will be critical for future breeding programs suited to eastern and north eastern parts of India where rice productivity is less than 40% of the national average due to acidic soil and poor availability of phosphorus.

The discovery of the PSTOL1 gene means that rice breeders will be able to breed new rice varieties faster and more easily, and with 100% certainty their new rice will have the gene.

Dr. Joko Prasetiyono, of the Institute for Agricultural Biotechnology and Genetic Resources Research and Development in Indonesia, is breeding rice plants with the PSTOL1 gene. The plants are not genetically modified just bred using smart modern breeding techniques.

“In field tests in Indonesia and the Philippines, rice with the PSTOL1 gene produced about 20% more grain than rice without the gene,” said Heuer.  “In our pot experiments,” she added, “when we use soil that is really low in phosphorus, we see yield increases of 60% and more, suggesting it will be very effective in soils low in phosphorus such as in upland rice fields that are not irrigated and where farmers are often very poor.”

The PSTOL1 gene is also being tested in rice varieties for the more productive irrigated rice-growing areas and initial results show that the plants grow a better root system and have higher production too. This means it could help farmers in these areas reduce their fertiliser use and expenditure without compromising productivity.

The discovery also demonstrates the importance of conserving the genetic diversity of traditional crop varieties such as Kasalath. IRRI conserves more than 114,000 different types of rice in the International Rice Genebank.

The group of rice (the aus-type) that Kasalath is part of is also the source of the submergence tolerance gene, which IRRI has used to breed submergence-tolerant (Sub1) rice varieties that are being widely adopted across Asia.

New rice varieties with the enhanced capacity to take up phosphorus may be available within a few years to farmers.

This research has been conducted in collaboration with JIRCAS, the University of Milano in Italy, the University of the Philippines Los Baños, and the Institute for Agricultural Biotechnology and Genetic Resources Research and Development in Indonesia. The main financial support was provided by the CGIAR Generation Challenge Program (GCP), with supplementary funding from other donors.